Transcriptomic analysis of ZMO_0422 in Zymomonas mobilis
Ontology highlight
ABSTRACT:
ORGANISM(S): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
PROVIDER: GSE304389 | GEO | 2025/11/20
REPOSITORIES: GEO
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| GSE304389_20250627_Kiley_RsuR_RNAseq_FPKM.txt.gz | Txt | |||
| GSE304389_20250627_Kiley_RsuR_RNAseq_HTSeq_raw_counts.txt.gz | Txt |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:Zymomonas mobilis is an important bioenergy organism that has potential to produce biofuels, including ethanol, in high volumes. Here we examined the response of Zymomonas mobilis to various oxidative stresses using genome-scale transcriptomics data. We first examined the transcrpit abundance in WT aerobic growth compared to aerobic grown in paraquat, which forms superoxide. Under anaerobic growth conditions we compared WT Zymomonas mobilis with strains grown in media lacking iron as well as strains lacking iron that were treated with the iron chelator DIP before collection. Finally we examined transcript abundance in cells lacking ZMO_0422 (Rrf2 family transcription factor homolog) and ZMO_1411 (Fur homolog) grown under anaerobic conditions.
2025-11-20 | GSE304360 | GEO
Project description:This study is aimed for the identification of novel small RNAs under different ethanol producing conditions. We have applied transcriptome analysis to facilitate identification and validation of 15 novel sRNAs in Zymomonas mobilis. We furthermore characterize their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4 and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed respectively. These data suggests that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses. Z. mobilis was grown under aerobic and anaerobic conditions which showed low and high ethanol production, respectively. Each samples were sequenced for identification of small RNA candidates and differentially expressed candidates between two conditions.
2014-05-20 | E-GEOD-57773 | biostudies-arrayexpress
Project description:This study is aimed for the identification of novel small RNAs under different ethanol producing conditions. We have applied transcriptome analysis to facilitate identification and validation of 15 novel sRNAs in Zymomonas mobilis. We furthermore characterize their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4 and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed respectively. These data suggests that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.
2014-05-20 | GSE57773 | GEO
Project description:Investigation of whole-genome gene expression level changes in RDM-4 strain of Zymomonas mobilis respiration-deficient mutant compared to the wild-type strain. The mutant strains were isolated from the antibiotics-resistant mutants of Z. mobilis ZM6. The RDM strains exhibited much higher ethanol fermentation abilities than the wild-type strain under aerobic conditions. The strains also gained thermotolerance and exhibited higher ethanol productivities at high temperature (39 ºC) under both non-aerobic and aerobic conditions compared with the wild-type strain. To evaluate the mechanisms of aerobic fermentation and thermotolerance of the RDM strain, we performed the microarray experiments.
2010-10-01 | GSE22355 | GEO
Project description:Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to ethanol stress. A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 5% ethanol. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.
2013-12-31 | E-GEOD-39558 | biostudies-arrayexpress
Project description:Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to furfural stress. A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 1.0 g/l furfural. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.
2012-05-08 | E-GEOD-37848 | biostudies-arrayexpress
Project description:Zymomonas mobilis ZM4 produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. However, the genetic and physiological basis of the ZM4 response to various industrially-relevant stresses is poorly understood. In this study, the dynamics of ZM4 oxygen stress responses were elucidated by characterizing the transcriptomic and metabolomic profiles of aerobic and anaerobic fermentations using whole-genome microarray analysis and gas chromatography-mass spectrometry. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Under aerobic conditions, much less ethanol was observed with other end-products produced, including acetate, lactate, and acetoin. In the early exponential phase, no genes were detected as being significantly differentially expressed between aerobic and anaerobic conditions via microarray analysis. However, microarray analysis of the stationary phase cultures revealed that 166 genes were significantly differentially expressed by more than two-fold. Quantitative-PCR validated the expression values for seventeen genes from different categories of stationary phase microarray data. Transcripts for Entner-Doudoroff pathway genes and gene pdc, encoding a key enzyme leading to the ethanol production, were at least 30-fold more abundant under anaerobic conditions at stationary phase based on quantitative-PCR results. Expression of stress response genes was found to be greater under oxygen stress conditions. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 under anaerobic conditions contained lower levels of amino acids, glucose and ED pathway intermediates, whereas metabolites such as ribitol, trehalose, myristic acid, glyceric acid, glucose 6-phosphate, mannose 6-phosphate, and 4-hydroxybutanoic acid were more abundant than under aerobic conditions. Transcriptomic and metabolomic data were consistent with faster glucose consumption and greater ethanol production under anaerobic conditions and suggested gene targets for deletion and improved fermentation. Keywords: Time course/ Stress Response A total of 24 samples were analyzed. These consisted of two times points, (3 hours and 26 hours) under two conditions (anaerobic and aerobic). There were 3 biological replicates and two dye swaps. Each microarray containted one to two probes per predicted coding sequence.
2010-05-18 | E-GEOD-10302 | biostudies-arrayexpress
Project description:Investigation of whole-genome gene expression level changes in RDM-4 strain of Zymomonas mobilis respiration-deficient mutant compared to the wild-type strain. The mutant strains were isolated from the antibiotics-resistant mutants of Z. mobilis ZM6. The RDM strains exhibited much higher ethanol fermentation abilities than the wild-type strain under aerobic conditions. The strains also gained thermotolerance and exhibited higher ethanol productivities at high temperature (39 ºC) under both non-aerobic and aerobic conditions compared with the wild-type strain. To evaluate the mechanisms of aerobic fermentation and thermotolerance of the RDM strain, we performed the microarray experiments. A four-chip study using total RNA recovered from the shaking cultures of wt and RDM-4 strains grown at 30ºC, a non-aerobic culture of wt strain grown at 30ºC, and a non-aerobic culture of RDM-4 strain grown at 38ºC. Each chip measures the expression level of 1,998 genes from Z. mobilis.
2010-10-01 | E-GEOD-22355 | biostudies-arrayexpress
Project description:Zymomonas mobilis ZM4 produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. However, the genetic and physiological basis of the ZM4 response to various industrially-relevant stresses is poorly understood. In this study, the dynamics of ZM4 oxygen stress responses were elucidated by characterizing the transcriptomic and metabolomic profiles of aerobic and anaerobic fermentations using whole-genome microarray analysis and gas chromatography-mass spectrometry. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Under aerobic conditions, much less ethanol was observed with other end-products produced, including acetate, lactate, and acetoin. In the early exponential phase, no genes were detected as being significantly differentially expressed between aerobic and anaerobic conditions via microarray analysis. However, microarray analysis of the stationary phase cultures revealed that 166 genes were significantly differentially expressed by more than two-fold. Quantitative-PCR validated the expression values for seventeen genes from different categories of stationary phase microarray data. Transcripts for Entner-Doudoroff pathway genes and gene pdc, encoding a key enzyme leading to the ethanol production, were at least 30-fold more abundant under anaerobic conditions at stationary phase based on quantitative-PCR results. Expression of stress response genes was found to be greater under oxygen stress conditions. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 under anaerobic conditions contained lower levels of amino acids, glucose and ED pathway intermediates, whereas metabolites such as ribitol, trehalose, myristic acid, glyceric acid, glucose 6-phosphate, mannose 6-phosphate, and 4-hydroxybutanoic acid were more abundant than under aerobic conditions. Transcriptomic and metabolomic data were consistent with faster glucose consumption and greater ethanol production under anaerobic conditions and suggested gene targets for deletion and improved fermentation. Keywords: Time course/ Stress Response
2008-10-10 | GSE10302 | GEO
Project description:Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to ethanol stress.
2013-12-31 | GSE39558 | GEO